+Open data
-Basic information
Entry | Database: PDB / ID: 1gp7 | ||||||
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Title | Acidic Phospholipase A2 from venom of Ophiophagus Hannah | ||||||
Components | PHOSPHOLIPASE A2 | ||||||
Keywords | HYDROLASE / PHOSPHOLIPASE A2 / SNAKE VENOM / KING COBRA / CARDIOTOXIC ACTIVITY / MYOTOXIC ACTIVITY / PANCREATIC LOOP / LIPID DEGRADATION / CALCIUM | ||||||
Function / homology | Function and homology information phospholipase A2 activity => GO:0004623 / phospholipase A2 activity => GO:0004623 / phospholipase A2 activity / phospholipase A2 / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / toxin activity / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | OPHIOPHAGUS HANNAH (king cobra) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Zhang, H. / Lin, Z. | ||||||
Citation | |||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gp7.cif.gz | 84.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gp7.ent.gz | 64.2 KB | Display | PDB format |
PDBx/mmJSON format | 1gp7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gp7_validation.pdf.gz | 444 KB | Display | wwPDB validaton report |
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Full document | 1gp7_full_validation.pdf.gz | 452 KB | Display | |
Data in XML | 1gp7_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 1gp7_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/1gp7 ftp://data.pdbj.org/pub/pdb/validation_reports/gp/1gp7 | HTTPS FTP |
-Related structure data
Related structure data | 1poaS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 16456.701 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: SNAKE VENOM / Source: (natural) OPHIOPHAGUS HANNAH (king cobra) / Tissue: VENOM / References: UniProt: P80966, phospholipase A2 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.21 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 100 MM HEPES PH 7.5, 4% ETHYLENE GLYCOL, 5% PEG4000 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K / Method: vapor diffusion, hanging dropDetails: Wang, Z., (2001) Acta Crystallogr.,Sect.D, D57, 709. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 12793 / % possible obs: 93.8 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 5 / % possible all: 75 |
Reflection | *PLUS Num. obs: 11965 / Num. measured all: 32758 |
Reflection shell | *PLUS % possible obs: 75 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1POA Resolution: 2.6→8 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.3352 Å2 / ksol: 0.471988 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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